The solid phase synthesis of DNA oligomers requires the orthogonal protection of the 5′ hydroxyl and exocyclic amines on cytosine, adenine and guanine.i,ii Most commonly, the 5′ hydroxyl group is protected as the acid labile dimethoxytrityl ether that is removed every synthetic cycle in order to expose the hydroxyl for coupling. The amines on the other hand are protected as amides that are stable to all the reagents of the synthetic cycle and are removed at the end of the synthesis using basic conditions. However the requirements for synthesis of RNA and DNA analogs containing base sensitive modifications have led to the development of alternate protection strategies. For instance Scaringe et aliii have used a trimethoxytrityl protection of nucleobases along with silyl protection of 5′ hydroxyl group. A different approach has resulted in the design of amide based protecting groups that are removable under very mild basic conditions or using nucleophiles.iv Nevertheless each of these methods has certain limitations. The trimethoxytrityl (TMTr or TMT) approach is clearly unsuited for use with 5′-dimethoxytrityl (DMT or DMTr) protection, which remains the most convenient protection group for the 5′ hydroxyl moiety. At the same time the use of amides removable under mild conditions is based on faster deprotection of the exocyclic amines in presence of base labile modifications. This approach is not generalizable in practice as the time for deprotection is dependent on the composition of the bases and the length of the oligonucleotide. Many of these groups such as phenoxyacetyl,v,vi allyloxycarbonylvii and 2,2′-bis(2-nitrophenyl)ethoxy-carbonylviii are also prone to side reactions such as transamidations during the capping step. Finally all amide based protecting groups are unsuitable for the synthesis of borane containing oligonucleotide analogs where the borane reagents convert amines irreversibly to alkyl and aryl amines.
Accordingly, there is a continuing need for a protecting group on exocyclic amines in nucleobases that can be selectively removed under a relatively mild condition.